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Pre-release

@a-ludi a-ludi released this Mar 17, 2020

[1.0.0-beta.1] - 2020-03-17

Added

  • post-consensus alignment and validation with new parameter
    --max-insertion-error
  • inserted sequences are highlighted by upper-case letters which can be
    turned off with --no-highlight-insertions
  • batch ranges may end with a $ indicating the end of the pileup DB
  • some mechanisms for early error detection
  • write duplicate contig IDs to contig alignment cache for easier debugging
  • added support for complementary contig alignments in check-results
  • allow .db databases as reference
  • improved version reporting
  • updated README with additional instructions

Changed

  • integrated Snakemake workflow into a single file and removed "testing"
    workflow
  • cropping and splicing of insertions:
    • existing sequence is completely retained
    • moved from process-pile-ups to output
    • binary format of insertions DBs (breaking change) to gain more freedom
      in later steps
    • splice sites are chosen based on the post-consensus alignments
  • ambiguities in the alignment of reads are now detected globally
  • weakly anchored alignments are discarded early in the filtering pipeline
  • the self- and read-alignment-based masks are now computed separately
  • coverage values may now be fractional
  • improved README by adhering to Standard Readme
  • better (error) reporting
  • temporary files have more informative names
  • many minor refactorings and extensions

Removed

  • combined self- and read-alignment-based masking: old behvaiour can be copied
    by using the --mask parameter and supplying both masks to all commands

Fixed

  • trying all possible reference reads for consensus in order to find a
    non-failing reference
  • corrected insertion splicing in case of reverse-complement alignment of the
    consensus
  • bug that caused check-results to discard all alignments in certain loci
  • added missing logic for cropped contigs in getGapState in check-results
Assets 3

@a-ludi a-ludi released this Jan 3, 2019 · 262 commits to master since this release

Added

  • work-around for damapper bug
  • histograms generated by check-results include a column for .999 sequence identity
  • check-results optionally writes a detailed gap report

Changed

  • simplified the coverage bounds interface of mask-repetitive-regions: only max-values and/or the read coverage are required
  • improve consensus quality by using lasfilteralignments to remove deteriorating local alignments
  • reduced value of --min-reads-per-pile-up to --min-spanning-reads (default: 3) to better work with extremely low coverage
  • reduced the default minimum anchor length to 500
  • fix & simplify score function for read alignments
  • suppress generation of two las files for reads alignment in generate-dazzler-options
  • insertion DBs do not include information about existing contigs anymore which makes validation of results easier
  • renamed debug-graphdebug-scaffold for clarity
  • added logging for discarded pile ups
  • check-results counts complementary alignments (inversions) as errors
  • remove leading/trailing gaps from all checks by check-results
  • improved quality of documentation
Assets 2
Pre-release
Pre-release

@a-ludi a-ludi released this Oct 15, 2018 · 309 commits to master since this release

Added

  • implemented routine to generate exact alignments from .las alignment chains
  • better conflict handling for scaffold graph (see --min-spanning-reads and
    --best-pile-up-margin)
  • resolve conflicting cropping information attached to contigs
  • accept both .db and .dam files
  • new pipeline command process-pile-ups to compute consensus in parallel
  • introduced build config testing which produces additional commands for
    evaluation of results:
    • translocate-gaps
    • find-closable-gaps
    • translate-coords
    • check-results
  • improved logging in general
  • output of assembly graph using --debug-graph
  • sorted CLI options alphabetically
  • inspect Dazzler masks using show-mask command
  • separate command mask-repetitive-regions for masking
  • show-* commands have --json switch
  • CLI switch --usage
  • runtime improvements
  • improved type definitions for better debugging experience
  • many small bug fixes
Assets 2
Aug 22, 2018
First working version which will undergo further testing.
Aug 13, 2018
initial commit
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